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Sample GSM3017853 Query DataSets for GSM3017853
Status Public on Dec 26, 2019
Title KP156
Sample type RNA
 
Source name Medium Arsenic exposed subjects (Mean Urinary As. 84.77±9.36 µg/g.creat)
Organism Homo sapiens
Characteristics tissue: Whole Blood
gender: Female
age group: 40 or Above
smoking status: Non smokers
residence type: Rural
Treatment protocol Freshly taken blood samples were taken RNA later and within two hours of samples collection, samples were stored at -80C
Extracted molecule total RNA
Extraction protocol RNA from the samples taken in RNA later was isolated using Ambion Ribopure-Blood RNA Kit (Cat#AM1928) as per manufacturer guidelines. Extracted RNA was quantified using Nanodrop-1000 Spectrophotomer and RNA quality was checked through Agilent 2100 Bioanalyzer
Label Cy3
Label protocol Cyanine-3 (Cy3) labelled cRNA was prepared from 200ng Total RNA using Agilent one colour Quick Amp Labeling kit according to manufacturer protocol followed by Qiagen RNAeasy Column Purification. Purified cRNA yeild was measured through Nanodrop-1000 Spectrophotometer
 
Hybridization protocol 600ng of Cy3 Labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1X Agilent Fragmentation Buffer, 10X Blocking Agent followed by 25µl of 2X Hi-RPM Hybridization buffer to stop the fragmentation reaction as per manufacturer guidelines for Agilent Sureprint G3 Human GE Kit 8 x 60K V2 G4851B Microarrays. Hybridization Assembly wase made as per guidelines of Agilent microarrays Hybridization Chamber User guide (G2534-90001). 40µl of Hybridized sample was loaded on slide in Chamber and Incubated for 17 hours in Hybridization oven at 65°C. Gene expression wash buffers containg 10% Triton-X102 were used for washing. Microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation
Scan protocol Immediately after washing, slides were scanned on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides. Pixel intensities were extracted as raw data from the scan images using Agilent Feature Extraction Software (Agilent) using default parameters
Description Peripheral Blood Stored in RNA later
Gene expression analysis of rural subjects exposed to elevated Arsenic levels in drinking water
Data processing All arrays were checked for their quality using ArrayQC (https://github.com/BiGCAT-UM/arrayQC_Module/), a quality control pipeline in R (version 2.10.1; The R Foundation for Statistical Computing, Vienna, Austria). For each spot the following steps were taken: local background correction, flagging of bad spots, controls and spots with too low intensity, log2 transformation, and quantile normalization. We filtered out control probes and low expressed probes. To get an idea of how bright expression probes should be, we computed the 95% percentile of the negative control probes on each array. We kept probes that are at least 10% brighter than the negative controls on at least 18 arrays (i.e. smallest number of subjects per exposure group). Next the avereps function was used to average replicate spots.
 
Submission date Feb 20, 2018
Last update date Dec 26, 2019
Contact name Muhammad Yasir Abdur Rehman
E-mail(s) mahryasir@gmail.com
Phone +923515357447
Organization name Quaid-i-Azam University
Department Environmental Sciences
Lab Environmental Health Laboratory
Street address 1
City Islamabad
State/province ICT
ZIP/Postal code 45320
Country Pakistan
 
Platform ID GPL17077
Series (1)
GSE110852 Gene expression profiles of subjects exposed to Arsenic through drinking water in Pakistan

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_23_P117082 10.73723813
A_33_P3246448 4.970369027
A_33_P3318220 4.799577831
A_33_P3236322 4.742573258
A_33_P3319925 5.093346403
A_21_P0000509 5.819358779
A_21_P0000744 7.111120958
A_24_P215804 6.122004075
A_23_P110167 9.101748009
A_33_P3211513 7.929898908
A_33_P3788124 3.954881411
A_33_P3414202 11.95652849
A_33_P3316686 9.077936303
A_33_P3300975 6.396580639
A_33_P3263061 9.028774612
A_33_P3261373 5.177581893
A_24_P278460 8.596053691
A_21_P0013109 4.873320752
A_21_P0014651 6.532795317
A_24_P286898 6.009821602

Total number of rows: 32828

Table truncated, full table size 811 Kbytes.




Supplementary file Size Download File type/resource
GSM3017853_US10063773_253949449065_S01_GE1_107_Sep09_2_3.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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